As a freelancer, I work in a lot of different code repos. Almost every team I work with has different ideas of how code should be organized, maintained, and structured. Now, I’m not here to start a battle about tabs versus spaces or alphabetical order of CSS properties versus organizing in terms of concerns (positioning styles, then element layout styles, then whatever else), because I’m honestly not attached to any one system anymore.
Part of getting comfortable with the command line is making it your own. Small customizations, shortcuts, and time saving techniques become second nature once you spend enough time fiddling around in your terminal. Since Git is my Version Control System of choice (due partially to its incredible popularity via GitHub), I like to spend lots of time optimizing my experience there.